P474: FUNCTIONAL (PHOSPHO-)PROTEOMICS OF DRUG RESPONSE IN ACUTE MYELOID LEUKEMIA
Authors: Denys Oliinyk, Maximilian Fleischmann, Dilfuza Ernafasova, Caroline Tschernjawski, Sebastian Scholl, Andreas Hochhaus, Florian Meier-Rosar
Journal: HemaSphere (2023)

Background: Acute Myeloid Leukemia (AML) is a particularly heterogeneous malignancy, for which standard care often fails to reach a durable response. Given the high inter-individual diversity, patients could potentially benefit from therapies tailored to an individual’s unique molecular profile, background and physical status. Such efforts are currently pioneered by genomics technologies, yet most therapeutics aim to alter the activity of proteins rather than genes. At the same time, our knowledge about the functional consequences of genetic aberrations and the role of the cellular context remains incomplete. Therefore, directly assessing how therapeutics alter the proteome activity will open new frontiers. Aims: Here, we introduce a functional mass spectrometry-based (phospho-)proteomics approach and demonstrate its application to probe the dynamic molecular response of AML cells to drug treatment. Methods: We build on a state-of-the-art high-resolution mass spectrometry platform to perform multi-modal proteome analyses from 96 well-plate cultures of cell lines. Viable primary peripheral blood mononuclear cells were isolated from patient blood draws. For drug response experiments, human cell lines were incubated with either DMSO or commonly available drugs (e.g. bortezomib, venetoclax) at IC50 concentrations following standard protocols. To quantify protein phosphorylation on a proteome-wide scale, we applied our recently developed µPhos protocol (Oliinyk et al., bioRxiv 2023) that enables straightforward and miniaturized sample processing from 96-well cell culture plates. To delineate drug response signatures, we performed dose-response and time-course experiments and analyzed the proteomics result files statistically in the R or Python programming environments. Results: We demonstrate the application of our µPhos platform to perform functional proteomics and phosphoproteomics of drug response in 96-well format. Using highly sensitive trapped ion mobility mass spectrometry, we quantified >15,000 unique phosphopeptides from 10 µg protein starting material (~50,000 human cancer cells) and generated quantitative profiles of >7,000 proteins within one hour analysis time. This analytical depth widely covers cellular pathways and clinically relevant drug targets. Analysis of primary AML cells revealed a remarkable diversity of phosphoproteomes between patients, indicating potential differences in their proteome activity status. Our cell culture experiments provided insight into the molecular signatures of drug response. For example, incubating the human AML cell line U937 with the proteasome inhibitor bortezomib showed a significant down-regulation of secretory proteins as well as increased phosphorylation of chromatin remodelers and the TGF-β signaling machinery. We are currently performing time-course and dose-response experiments to further deconvolute the complex response signatures. Summary/Conclusion: We conclude that µPhos is a powerful platform to elucidate drug response on the phosphoproteome level. The demonstrated capability to work with small sample amounts makes it also very attractive for the analysis of primary patient samples. Keywords: Bortezomib, Proteomics, Acute myeloid leukemia, Phosphorylation